[INFRASTRUCTURE] : Create infrastructure to support the ontology browsing tool

[gtsueng]

Name

Create infrastructure to support the ontology browsing tool

Description

The ontology/hierarchical browsing tool requires efficient retrieval of lineage information for the display of the lineage tree, but also to enable the aggregation of counts of records that match a term and the counts of records from each child term. The infrastructure should be flexible enough to work with different ontologies (as needed).

User studies have been conducted which indicate that users do like the suggestion to display counts of relevant records for each search term, with a preference for seeing both the count of the records for that term, and the count of the records for that term plus all child terms.

Other ontologies currently in use in the Discovery Portal

• species, infectiousAgent: NCBI Taxonomy
• topicCategory: EDAM Topics Ontology (latest, unstable version)
• healthCondition: MONDO, HPO, DO, NCIT

In the pipeline:

• measurementTechnique: Subset of MMO, CHMO, BAO, OBI, EFO, EDAM Topics, NCIT
• variableMeasured: TBD

WBS Task

https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/20
https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/4

Related Issues

• [UX Test]: Ontology Browser Tool Test nde-portal#261
• https://github.com/NIAID-Data-Ecosystem/niaid-feedback/issues/10

[gtsueng]

It was noticed in November that there are discrepancies between returns using the OLS API and the NCBI Taxonomy browser.

In NCBI, 3366610 is a child of 2157:
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=3366610&lvl=3&lin=f&keep=1&srchmode=1&unlock
In OLS: 3366610 is not in the children list of 2157:
https://www.ebi.ac.uk/ols4/api/ontologies/ncbitaxon/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCBITaxon_2157/children?&lang=en

Upon investigation, it appears that the discrepancy stems from a nomenclature status dispute between NCBI Taxon and GTDB https://en.wikipedia.org/wiki/Euryarchaeota#Nomenclatural_status

To resolve this discrepancy, we will update and use the Biothings Taxonomy API to perform organism queries.

[gtsueng]

The only improvements remaining in terms of ontology browser infrastructure for NCBI Taxonomy are:

• Having an exact match score higher than a partial match. Right now, if you search for M. tuberculosis, a large number of M. tuberculosis subspecies will appear and crowd out the actual M. tuberculosis species. This may be due to the API query results for all these subspecies having an equivalent or higher ES score than the exact match result.
• Improving the performance. Load times could potentially be improved, but this is likely NOT on the biothings Taxonomy end, rather on the Discovery Portal end.